Dear Daisuke, Thank you for your answer. I was looking at the 3D-SURFER server, it looks great. I'm only trying to compare pairs (or sometimes triplets) of proteins though. Is there a way to use 3D-SURFER for that purpose? And would it give me a 3D structural alignment of the binding sites?
Thanks, Sarah On Fri, Oct 31, 2014 at 4:46 PM, Daisuke Kihara <[email protected]> wrote: > Dear Sarah, > > we don't have a server for you to quickly use but our lab has methods for > alignment-free binding sites comparison by comparing pocket surface shape, > named Pocket-Surfer and Patch-Surfer. > > These are literature: > http://www.ncbi.nlm.nih.gov/pubmed/20455259 > http://www.ncbi.nlm.nih.gov/pubmed/22275074 > > http://bioinformatics.oxfordjournals.org/content/early/2014/10/29/bioinformatics.btu724.abstract > > If you are interested, I am happy to discuss what we can do for your > problem. > Sincerely, > Daisuke > ---- > Daisuke Kihara, Ph.D. > Professo > Department of Biological Sciences/Computer Science > Purdue University > West Lafayette, IN 47907 > http://kiharalab.org Tel: 1-765-496-2284 > > > > On Fri, Oct 31, 2014 at 3:48 PM, Sarah Barelier < > [email protected]> wrote: > >> Dear all, >> I'm sorry, this is a bit off-topic. I'm looking for a tool to compare >> pairs of binding sites. >> It doesn't need to be high-throughput, since I'll only be comparing ~100 >> pairs, but I'd like it to be robust and, more importantly, >> alignment-independent. >> Indeed, the binding sites I want to compare are not necessarily related >> in terms of amino-acid composition, but I'd like to still be able to detect >> similarities between them. >> Does anyone have suggestions? >> Thank you. >> >> Sarah >> >> -- >> Sarah Barelier, Ph.D. >> Postdoctoral Researcher >> Shoichet Lab, UCSF >> [email protected] >> >> Department of Pharmaceutical Chemistry >> 1700 4th Street, Byers Hall, Room N501 >> San Francisco, CA 94158-2550 >> > > > > -- > Daisuke > -- Sarah Barelier, Ph.D. Postdoctoral Researcher Shoichet Lab, UCSF [email protected] Department of Pharmaceutical Chemistry 1700 4th Street, Byers Hall, Room N501 San Francisco, CA 94158-2550
